diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index 58e423491429c502836118cdfa68bd71eb9b89a7..c14ea43a20fea23d1c9fe1801ed774125fe788c8 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -121,6 +121,11 @@ class lDDTScorer:
original residue numbers were.
:type seqres_mapping: :class:`dict` (key: :class:`str`, value:
:class:`ost.seq.AlignmentHandle`)
+ :param calpha: Only consider atoms with name "CA". Technically this sets
+ the expected atom names for each residue name to ["CA"], thus
+ invalidating *compound_lib*. No check whether the target
+ residues are actually amino acids!
+ :type calpha: :class:`bool`
:raises: :class:`RuntimeError` if *target* contains compound which is not in
*compound_lib*, :class:`RuntimeError` if *symmetry_settings*
specifies symmetric atoms that are not present in the according
@@ -132,7 +137,6 @@ class lDDTScorer:
(seq1 contains gaps, mismatch in seq1/seq2, seq2 does not match
residues in corresponding chains).
"""
-
def __init__(
self,
target,
@@ -141,6 +145,7 @@ class lDDTScorer:
sequence_separation=0,
symmetry_settings=None,
seqres_mapping=dict(),
+ calpha=False
):
self.target = target
@@ -152,6 +157,10 @@ class lDDTScorer:
else:
self.symmetry_settings = symmetry_settings
+ # whether to only consider atoms with name "CA", invalidates
+ # *compound_lib*
+ self.calpha=calpha
+
# names of heavy atoms of each unique compound present in *target* as
# extracted from *compound_lib*, e.g.
# self.compound_anames["GLY"] = ["N", "CA", "C", "O"]
@@ -202,7 +211,7 @@ class lDDTScorer:
# setup members defined above
self._SetupEnv(self.compound_lib, self.symmetry_settings,
- seqres_mapping)
+ seqres_mapping, self.calpha)
# distance related members are lazily computed as they're affected
# by different flavours of lDDT (e.g. lDDT including inter-chain
@@ -560,7 +569,8 @@ class lDDTScorer:
dummy_scorer = lDDTScorer(model.Select("cname="+ch_name),
self.compound_lib,
symmetry_settings = sm,
- inclusion_radius = self.inclusion_radius)
+ inclusion_radius = self.inclusion_radius,
+ calpha = self.calpha)
penalty += dummy_scorer.n_distances
return penalty
@@ -622,7 +632,8 @@ class lDDTScorer:
return rnums
- def _SetupEnv(self, compound_lib, symmetry_settings, seqres_mapping):
+ def _SetupEnv(self, compound_lib, symmetry_settings, seqres_mapping,
+ calpha):
"""Sets target related lDDTScorer members defined in constructor
No distance related members - see _SetupDistances
@@ -682,31 +693,10 @@ class lDDTScorer:
self.chain_res_start_indices.append(len(self.compound_names))
for r, rnum in zip(chain.residues, residue_numbers[ch_name]):
if r.name not in self.compound_anames:
- compound = compound_lib.FindCompound(r.name)
- if compound is None:
- raise RuntimeError(f"compound_lib has no entry for {r}")
- atom_names = list()
- for atom_spec in compound.GetAtomSpecs():
- if atom_spec.element not in ["H", "D"]:
- atom_names.append(atom_spec.name)
- self.compound_anames[r.name] = atom_names
- self.compound_symmetric_atoms[r.name] = list()
- if r.name in symmetry_settings.symmetric_compounds:
- for pair in symmetry_settings.symmetric_compounds[
- r.name
- ]:
- try:
- a = self.compound_anames[r.name].index(pair[0])
- b = self.compound_anames[r.name].index(pair[1])
- except:
- msg = f"Could not find symmetric atoms "
- msg += f"({pair[0]}, {pair[1]}) for {r.name} "
- msg += f"as specified in SymmetrySettings in "
- msg += f"compound from component dictionary. "
- msg += f"Atoms in compound: "
- msg += f"{self.compound_anames[r.name]}"
- raise RuntimeError(msg)
- self.compound_symmetric_atoms[r.name].append((a, b))
+ # sets compound info in self.compound_anames and
+ # self.compound_symmetric_atoms
+ self._SetupCompound(r, compound_lib, symmetry_settings,
+ calpha)
self.res_start_indices.append(current_idx)
self.res_mapper[(ch_name, rnum)] = len(self.compound_names)
@@ -729,6 +719,39 @@ class lDDTScorer:
)
self.n_atoms = current_idx
+ def _SetupCompound(self, r, compound_lib, symmetry_settings, calpha):
+ """fill self.compound_anames/self.compound_symmetric_atoms
+ """
+ if calpha:
+ # throw away compound_lib info
+ self.compound_anames[r.name] = ["CA"]
+ self.compound_symmetric_atoms[r.name] = list()
+ else:
+ atom_names = list()
+ symmetric_atoms = list()
+ compound = compound_lib.FindCompound(r.name)
+ if compound is None:
+ raise RuntimeError(f"no entry for {r} in compound_lib")
+ for atom_spec in compound.GetAtomSpecs():
+ if atom_spec.element not in ["H", "D"]:
+ atom_names.append(atom_spec.name)
+ self.compound_anames[r.name] = atom_names
+ if r.name in symmetry_settings.symmetric_compounds:
+ for pair in symmetry_settings.symmetric_compounds[r.name]:
+ try:
+ a = self.compound_anames[r.name].index(pair[0])
+ b = self.compound_anames[r.name].index(pair[1])
+ except:
+ msg = f"Could not find symmetric atoms "
+ msg += f"({pair[0]}, {pair[1]}) for {r.name} "
+ msg += f"as specified in SymmetrySettings in "
+ msg += f"compound from component dictionary. "
+ msg += f"Atoms in compound: "
+ msg += f"{self.compound_anames[r.name]}"
+ raise RuntimeError(msg)
+ symmetric_atoms.append((a, b))
+ self.compound_symmetric_atoms[r.name] = symmetric_atoms
+
def _SetupDistances(self):
"""Compute distance related members of lDDTScorer
"""
diff --git a/modules/mol/alg/tests/test_lddt.py b/modules/mol/alg/tests/test_lddt.py
index 0264b55f0a968f84d8bdee9698bb69814379d72e..0a0e365b1d2dff552ccfb4d45adc2ecae3f40776 100644
--- a/modules/mol/alg/tests/test_lddt.py
+++ b/modules/mol/alg/tests/test_lddt.py
@@ -148,6 +148,30 @@ class TestlDDT(unittest.TestCase):
scorer = lDDTScorer(target, conop.GetDefaultLib(),
sequence_separation=0)
+ def test_calpha(self):
+ model = _LoadFile("7SGN_C_model.pdb")
+ target = _LoadFile("7SGN_C_target.pdb")
+
+ # do scoring and select aname=CA
+ scorer = lDDTScorer(target.Select("aname=CA"),
+ conop.GetDefaultLib())
+ score_one, per_res_scores_one = scorer.lDDT(model)
+ score_two, per_res_scores_two = scorer.lDDT(model.Select("aname=CA"))
+
+ # no selection, just setting calpha flag should give the same
+ scorer = lDDTScorer(target,
+ conop.GetDefaultLib(),
+ calpha=True)
+ score_three, per_res_scores_three = scorer.lDDT(model)
+
+ # check
+ self.assertAlmostEqual(score_one, score_two, places=5)
+ self.assertAlmostEqual(score_one, score_three, places=5)
+ for a,b in zip(per_res_scores_one, per_res_scores_two):
+ self.assertAlmostEqual(a, b, places=5)
+ for a,b in zip(per_res_scores_one, per_res_scores_three):
+ self.assertAlmostEqual(a, b, places=5)
+
if __name__ == "__main__":
from ost import testutils
if testutils.SetDefaultCompoundLib():